Mercurial > repos > malex > tandem_repeats_finder

comparison trf_wrapper.py @ 1:2a3c8b2d5979 default tip

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Uploaded the wrapper file
author malex
date Wed, 30 Nov 2011 12:18:55 -0500
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0:7676570eb676 1:2a3c8b2d5979
1 #!/usr/bin/env python
2
3 """
4 Runs TRF on a sequence file.
5 For use with trf version 4.04
6
7 usage: trf_wrapper.py input_file <required parameters> [options]
8 Required parameters:
9 match
10 mismatch
11 indels
12 match_probability (%, 10-100)
13 indel_probability (%, 10-100)
14 minimal score (30-150)
15 maximum period size (1-2000)
16 """
17
18 import optparse, os, shutil, subprocess, sys, re
19 from os.path import abspath
20
21 def remove_bgcolor(infilename,outfilename):
22 infile = open(infilename, "r")
23 outfile = open(outfilename, "w")
24 bgcolor = re.compile(r'FBF8BC')
25 for line in infile:
26 line = bgcolor.sub('FFFFFF', line)
27 outfile.write(line)
28 infile.close()
29 outfile.close()
30 os.remove(infilename)
31
32 def remove_html(infilename,outfilename):
33 infile = open(infilename, "r")
34 outfile = open(outfilename, "w")
35 opena = re.compile(r'<A\ HREF.*?>')
36 bgcolor = re.compile(r'FBF8BC')
37 closea = re.compile(r'</A>')
38 for line in infile:
39 line = opena.sub('', line)
40 line = bgcolor.sub('FFFFFF', line)
41 line = closea.sub('', line)
42 outfile.write(line)
43 infile.close()
44 outfile.close()
45 os.remove(infilename)
46
47 def stop_err(msg):
48 sys.stderr.write("%s\n" % msg)
49 sys.exit()
50
51 def __main__():
52 #Parse arguments
53 usage = "usage: %prog input match mismatch indels match_p indel_p min_score max_period [options]"
54 parser = optparse.OptionParser(usage)
55 parser.add_option( '-f', '--flanking', dest='flanking', action='store_true', help='Flanking sequence' )
56 parser.add_option( '-m', '--masked', dest='masked', action='store_true', help='Masked sequence' )
57 parser.add_option( '-r', '--redundancy', dest='redundancy', action='store_true', help='No redundance elimination' )
58 parser.add_option( '-o', '--datoutput', dest='datoutput', action='store', help='Output data file name' )
59 parser.add_option( '-k', '--maskoutput', dest='maskoutput', action='store', help='Output mask file name' )
60 parser.add_option( '-t', '--report', dest='report', action='store', help='Report file name' )
61 parser.add_option( '-i', '--indices', dest='indices', action='store', help='Indices file name' )
62 (opts, arguments) = parser.parse_args()
63
64 # Arguments and options
65 if len(arguments) != 8:
66 print(usage)
67 stop_err('Wrong number of arguments passed')
68 output_dat = "%s.%s.%s.%s.%s.%s.%s.%s.dat" % (tuple(arguments))
69 output_mask = "%s.%s.%s.%s.%s.%s.%s.%s.mask" % (tuple(arguments))
70 output_report = "%s.%s.%s.%s.%s.%s.%s.%s.1.html" % (tuple(arguments))
71 output_indices = "%s.%s.%s.%s.%s.%s.%s.%s.1.txt.html" % (tuple(arguments))
72
73 if opts.masked and opts.masked == True:
74 arguments.append('-m')
75 if opts.flanking and opts.flanking == True:
76 arguments.append('-f')
77 if opts.redundancy and opts.redundancy == True:
78 arguments.append('-r')
79 if opts.datoutput and opts.datoutput != '':
80 output_dat_filename = opts.datoutput
81 if opts.maskoutput and opts.maskoutput != '':
82 output_mask_filename = opts.maskoutput
83 if opts.report and opts.report != '':
84 output_report_filename = opts.report
85 if opts.indices and opts.indices != '':
86 output_indices_filename = opts.indices
87
88 # Run
89 cmd = arguments
90 cmd.insert(0,"trf")
91 # Produce both html and dat files
92 cmd.append("-d")
93 try:
94 proc = subprocess.Popen(args=cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
95 except Exception, err:
96 sys.stderr.write("Error invoking command: \n%s\n\n%s\n" % (cmd, err))
97 sys.exit(1)
98 stdout, stderr = proc.communicate()
99 return_code = proc.returncode
100 if return_code != 1:
101 sys.stdout.write(stdout)
102 sys.stderr.write(stderr)
103 sys.stderr.write("Return error code %i from command:\n" % return_code)
104 sys.stderr.write("%s\n" % cmd)
105 else:
106 sys.stdout.write(stdout)
107 sys.stdout.write(stderr)
108 cdir = os.getcwd()
109 file_list = os.listdir(cdir)
110 try:
111 report_file = os.path.basename(output_report)
112 indices_file = os.path.basename(output_indices)
113 remove_html(report_file, output_report_filename)
114 remove_bgcolor(indices_file, output_indices_filename)
115 shutil.move(os.path.basename(output_dat), output_dat_filename)
116 # shutil.copyfile(os.path.basename(output_report), output_report_filename)
117 # shutil.copyfile(os.path.basename(output_indices), output_indices_filename)
118 if opts.masked and opts.masked == True:
119 shutil.move(os.path.basename(output_mask), output_mask_filename)
120 except Exception, err:
121 sys.stderr.write("Error copying output files: \n%s\n" % err)
122 if __name__=="__main__": __main__()